In recent years, navigation by stellar refraction has received considerable attention, having advantages of high accuracy, simple construction, and low cost. Nevertheless, there are many limitations to the precision and application of this method using a traditional measurement model. This article studies the changing pattern of atmospheric density, the disturbed atmospheric density model and measurement model of stellar refraction ranging from 20 km to 50 km. Furthermore, a control algorithm of multiple mode switching and an adaptive measurement model are proposed. With this method, any refracted starlight from the scope of between 20 km and 50 km can be captured and the measurement model at the appropriate height can be automatically established. Due to this, the reliability and practicality of navigation have been raised considerably. Accuracy of navigation using the adaptive measurement method is observed to improve by about 14%, using computer simulation based on an Unscented Kalman Filter (UKF).